Genomic Characterization of KPC-31 and OXA-181 Klebsiella pneumoniae Resistant to New Generation of β-Lactam/β-Lactamase Inhibitor Combinations

Abstract

Background: Carbapenem resistant Klebsiella pneumoniae (cr-Kp) causes serious infections associated with a high mortality rate. The clinical efficacy of ceftazidime/avibactam (CZA), meropenem/vaborbactam (M/V), and imipenem/relebactam (I/R) against cr-Kp is challenged by the emergence of resistant strains, making the investigation and monitoring of the main resistance mechanisms crucial. In this study, we reported the genome characterization of a Klebsiella pneumoniae strain isolated from a critically ill patient and characterized by a multidrug resistant (MDR) profile, including resistance to CZA, M/V, and I/R. Methods: An antimicrobial susceptibility test (AST) was performed by an automated system and E-test and results were interpreted following the EUCAST guidelines. Genomic DNA was extracted using a genomic DNA extraction kit and it was sequenced using the Illumina Nova Seq 6000 platform. Final assembly was manually curated and carefully verified for detection of antimicrobial resistance genes, porins modifications, and virulence factors. Results: The K. pneumoniae isolate belonged to sequence type ST512 and harbored 23 resistance genes, conferring resistance to all antibiotic classes, including blaKPC-31 and blaOXA-181, leading to carbapenems resistance. The truncation of OmpK35 and mutation OmpK36GD were also observed. Conclusions: The genomic characterization demonstrated the high resistant profile of new cr-Kp coharboring class A and D carbapenemases. The presence of KPC-31, as well as the detection of OXA-181 and porin modifications, further limit the therapeutic options, including the novel combinations of β-lactam/β-lactamase inhibitor antibiotics in patients with severe pneumonia caused by cr-Kp.

A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy

“…According to international guidelines, a protocol for monitoring antibiotic resistance has been active in our hospital since 2015. As already described in previous reports [ 13 , 41 ], the local epidemiological scenario has shown an increased variability in terms of circulating variants, particularly among carbapenemase-producing Gram-negative bacteria, such as Escherichia coli bla VIM and Enterobacter spp. class A carbapenemase producers.…”

In vitro mimicry of in vivo KPC mutations by ceftazidime-avibactam: phenotypes, mechanisms, genetic structure and kinetics of enzymatic hydrolysis

“…However, with its widespread use in clinical practice, we were alarmed by the explosion in the detection of bla KPC-2 or bla KPC-3 mutants after ceftazidime-avibactam treatment. Most of these mutants showed high-level resistance to ceftazidime-avibactam, such as bla KPC-31 [ 27 ], bla KPC-33 [ 20 ], etc. Moreover, the increased bla KPC expression, membrane porin deficiency and the co-production of KPC variants and other carbapenemases could mediate both carbapenem and ceftazidime-avibactam resistance [ 44 , 45 ].…”

“…The bla KPC variants tend to have a distinctive antimicrobial susceptibility phenotype. The majority of KPC mutants exhibit the ability to confer resistance to ceftazidime-avibactam (MIC range 16 - > 128 mg/L), mainly through the enhanced hydrolytic activity towards ceftazidime such as bla KPC-31 [ 27 ], bla KPC-41 [ 29 ] and reduced inhibition ability of avibactam such as bla KPC-109 [ 28 ]， bla KPC-53 [ 19 ]. To note, most KPC variants could mediate susceptibility to carbapenems (especially imipenem) other than bla KPC-87 [ 30 ], bla KPC-109 [ 28 ] and so on.…”

Identification of a Novel KPC Variant, KPC-204, Conferring Resistance to Both Carbapenems and Ceftazidime–Avibactam in an ST11 Klebsiella pneumoniae Strain

“…Simultaneous resistance to CZA and MEM is rare. Muresu et al reported [ 39 ] a K. pneumoniae strain harboring bla KPC-31 and bla OXA-181 that was resistant to both CZA and MEM, but the cloning of bla KPC-31 [ 40 ] and bla OXA-181 [ 41 ] did not show MEM resistance. Arcari et al reported [ 42 ] a K. pneumoniae strain carrying bla KPC-154 that showed MEM resistance, but resistance was not observed when the bla KPC-154 gene was cloned.…”